Primary prevention of C. difficile infection (CDI) is a priority for hospitals and probiotics have the potential to interfere with colonization and/or infection with C. difficile offering an opportunity to enhance ongoing primary prevention strategies. The overall objective of this study was to evaluate the impact of a hospital-wide computerized clinical decision support system tool to prescribe probiotics to eligible adult patients receiving antibiotics for the primary prevention of CDI. After implementation of the tool, the odds of CDI was 1.41 in eligible patients compared to the pre-intervention time period (aOR 1.41, 95% CI 1.11, 1.79). A propensity score matched analysis showed that patients who received probiotics did not have lower rates of CDI compared to those who did not (OR 1.46, 95% CI 0.87, 2.45). Based on these findings, the use of probiotics for the primary prevention of CDI is not supported.